Starting /dee2/code/volunteer_pipeline.sh ERR6133531 current disk space = 1544513150976 free memory = 1598273748 ERR6133531 SRAfilesize 4cff26eb780058a773af0f1defd6f280 ERR6133531.sra ERR6133531.sra file validated ERR6133531 is single end ERR6133531 is conventional basespace ERR6133531 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133531_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.69775 33.0 33.0 37.0 27.0 37.0 2 35.84275 37.0 37.0 37.0 33.0 37.0 3 35.10175 37.0 33.0 37.0 33.0 37.0 4 35.212 37.0 37.0 37.0 33.0 37.0 5 35.17525 37.0 37.0 37.0 33.0 37.0 6 35.488 37.0 37.0 37.0 33.0 37.0 7 37.293 37.0 37.0 40.0 33.0 40.0 8 37.40225 37.0 37.0 40.0 33.0 40.0 9 37.2955 37.0 37.0 40.0 33.0 40.0 10-11 37.33225 37.0 37.0 40.0 33.0 40.0 12-13 37.296625 37.0 37.0 40.0 33.0 40.0 14-15 37.309375 37.0 37.0 40.0 33.0 40.0 16-17 37.210499999999996 37.0 37.0 40.0 33.0 40.0 18-19 37.1215 37.0 37.0 40.0 33.0 40.0 20-21 37.075500000000005 37.0 37.0 40.0 33.0 40.0 22-23 37.023 37.0 37.0 40.0 33.0 40.0 24-25 37.098124999999996 37.0 37.0 40.0 33.0 40.0 26-27 37.00475 37.0 37.0 40.0 33.0 40.0 28-29 36.92075 37.0 37.0 40.0 33.0 40.0 30-31 36.8425 37.0 37.0 40.0 33.0 40.0 32-33 36.760000000000005 37.0 37.0 40.0 33.0 40.0 34-35 36.56975 37.0 37.0 40.0 33.0 40.0 36-37 36.4595 37.0 37.0 40.0 33.0 40.0 38-39 36.457125 37.0 37.0 40.0 33.0 40.0 40-41 36.095 37.0 37.0 40.0 33.0 40.0 42-43 36.017624999999995 37.0 37.0 40.0 33.0 40.0 44-45 35.733125 37.0 35.0 38.5 33.0 40.0 46-47 35.3735 37.0 33.0 37.0 30.0 40.0 48-49 35.43675 37.0 33.0 37.0 33.0 40.0 50-51 35.344125 37.0 33.0 37.0 33.0 40.0 52-53 35.00375 37.0 33.0 37.0 27.0 40.0 54-55 35.0595 37.0 33.0 37.0 33.0 38.5 56-57 34.91675 37.0 33.0 37.0 30.0 37.0 58-59 34.223375000000004 37.0 33.0 37.0 27.0 37.0 60-61 34.465 37.0 33.0 37.0 27.0 37.0 62-63 34.357124999999996 37.0 33.0 37.0 27.0 37.0 64-65 34.407875000000004 37.0 33.0 37.0 27.0 37.0 66-67 34.37525 37.0 33.0 37.0 27.0 37.0 68-69 33.689375 35.0 33.0 37.0 27.0 37.0 70-71 33.742362640801005 35.0 33.0 37.0 27.0 37.0 72-73 34.12121412173454 37.0 33.0 37.0 27.0 37.0 74-75 34.069206678660834 37.0 33.0 37.0 27.0 37.0 76-77 34.01235626027618 37.0 33.0 37.0 27.0 37.0 78-79 34.06786523676482 37.0 33.0 37.0 27.0 37.0 80-81 33.94453974177597 37.0 33.0 37.0 27.0 37.0 82-83 33.84297753361446 37.0 33.0 37.0 27.0 37.0 84-85 33.73515646642105 37.0 33.0 37.0 27.0 37.0 86-87 33.65397350993378 37.0 33.0 37.0 27.0 37.0 88-89 33.77228731533367 37.0 33.0 37.0 27.0 37.0 90-91 33.532475802343356 37.0 33.0 37.0 27.0 37.0 92-93 33.50382068262863 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 15.0 22 22.0 23 23.0 24 31.0 25 36.0 26 38.0 27 50.0 28 54.0 29 64.0 30 77.0 31 118.0 32 144.0 33 172.0 34 231.0 35 418.0 36 926.0 37 1000.0 38 565.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.75 1.7500000000000002 2.275 6.225 2 74.375 14.899999999999999 6.225 4.5 3 38.05 37.9 12.75 11.3 4 34.599999999999994 28.825 17.150000000000002 19.425 5 24.675 31.8 24.575 18.95 6 21.25 39.825 23.05 15.875 7 36.775000000000006 29.225 19.375 14.625 8 31.924999999999997 30.099999999999998 21.9 16.075 9 27.875 28.349999999999998 26.575 17.2 10-11 27.250000000000004 27.1375 26.737499999999997 18.875 12-13 28.712500000000002 26.487500000000004 26.1125 18.6875 14-15 23.1125 29.45 28.449999999999996 18.987499999999997 16-17 24.8125 31.162499999999998 25.4625 18.5625 18-19 23.75 27.3625 27.1625 21.725 20-21 24.637500000000003 25.937500000000004 28.812500000000004 20.6125 22-23 27.375 24.0125 26.55 22.0625 24-25 26.2875 24.375 27.3 22.037499999999998 26-27 25.174999999999997 25.55 29.849999999999998 19.425 28-29 25.424999999999997 26.7625 27.8125 20.0 30-31 27.675 24.6625 26.5125 21.15 32-33 24.2875 27.0 26.924999999999997 21.7875 34-35 25.01876407305479 26.257192894671004 27.24543407555667 21.478608956717537 36-37 24.474999999999998 24.7 28.212500000000002 22.6125 38-39 26.775 25.412499999999998 29.175 18.637500000000003 40-41 27.12945590994372 25.265791119449656 26.67917448405253 20.925578486554098 42-43 26.11688149167814 27.43085971718183 25.89162808159179 20.560630709548242 44-45 25.01563477173233 25.390869293308317 28.855534709193247 20.737961225766107 46-47 24.5375 24.025 28.225 23.2125 48-49 24.956239059764943 24.643660915228807 30.48262065516379 19.91747936984246 50-51 25.5375 27.375 28.1875 18.9 52-53 23.761880940470235 27.40120060030015 27.688844422211105 21.14807403701851 54-55 22.7 28.6875 28.299999999999997 20.3125 56-57 26.8 25.7375 27.700000000000003 19.7625 58-59 23.599999999999998 24.4125 29.75 22.237499999999997 60-61 25.087500000000002 24.462500000000002 29.262500000000003 21.1875 62-63 22.8125 27.5875 31.175000000000004 18.425 64-65 22.6 27.8625 28.975 20.5625 66-67 24.4875 26.987499999999997 28.212500000000002 20.3125 68-69 22.475 26.8 28.050000000000004 22.675 70-71 24.690431519699814 26.516572858036273 28.305190744215135 20.48780487804878 72-73 25.914786967418546 24.072681704260653 28.671679197994987 21.340852130325814 74-75 24.80844115060922 25.97663610099234 29.01645521919357 20.198467529204876 76-77 22.406847935548843 25.981873111782477 28.159617321248742 23.451661631419938 78-79 23.709779179810724 25.741324921135643 29.198738170347006 21.350157728706627 80-81 23.294087859222685 28.358020002531966 29.826560324091655 18.52133181415369 82-83 23.3875063484002 25.342813610970033 29.2407313357034 22.02894870492636 84-85 24.318818436465495 23.949579831932773 30.735930735930733 20.995670995670995 86-87 22.30005094243505 26.502801833927663 31.96637799286806 19.230769230769234 88-89 21.281202241467142 27.903718797758533 31.202241467142127 19.612837493632195 90-91 26.069791136016303 26.031584309730004 28.03107488537952 19.867549668874172 92-93 22.24910850738665 28.71879775853286 29.99235863474274 19.039735099337747 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 4.0 18 5.5 19 2.0 20 0.0 21 2.0 22 3.5 23 5.5 24 5.5 25 4.5 26 8.0 27 9.0 28 15.0 29 22.0 30 23.5 31 29.0 32 41.5 33 58.0 34 67.5 35 84.5 36 98.5 37 126.0 38 183.5 39 186.0 40 173.0 41 187.5 42 207.0 43 223.0 44 195.5 45 172.0 46 205.0 47 204.5 48 174.5 49 174.5 50 164.0 51 151.0 52 135.0 53 148.0 54 151.5 55 108.0 56 66.5 57 47.0 58 50.0 59 47.5 60 43.5 61 43.5 62 40.0 63 35.5 64 35.5 65 36.0 66 30.5 67 19.5 68 12.5 69 12.0 70 9.0 71 7.0 72 4.0 73 4.0 74 4.0 75 1.5 76 1.5 77 0.5 78 0.5 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.075 36-37 0.0 38-39 0.0 40-41 0.0625 42-43 0.11249999999999999 44-45 0.0625 46-47 0.0 48-49 0.025 50-51 0.0 52-53 0.05 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 5.0 71 1.0 72 8.0 73 3.0 74 5.0 75 4.0 76 4.0 77 6.0 78 3.0 79 10.0 80 3.0 81 7.0 82 6.0 83 7.0 84 2.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3926.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.45 #Duplication Level Percentage of deduplicated Percentage of total 1 92.97700435052828 74.8 2 4.039776258545681 6.5 3 1.2119328775637042 2.9250000000000003 4 0.435052827843381 1.4000000000000001 5 0.3729024238657551 1.5 6 0.09322560596643878 0.44999999999999996 7 0.09322560596643878 0.525 8 0.15537600994406464 1.0 9 0.031075201988812924 0.22499999999999998 >10 0.5282784338098198 7.925 >50 0.06215040397762585 2.75 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 57 1.425 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 53 1.325 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 39 0.975 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 25 0.625 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 20 0.5 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 20 0.5 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 16 0.4 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 14 0.35000000000000003 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit GGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCGGCACCAGCTGCG 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAG 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 5 0.125 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGGTGTTGTAGGTCACCGAGGCTGTTCTGAGATTGCGACCAAGCACGTA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0125 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.037500000000000006 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197444 READS because READLEN < 1 Read 197444 spots for ERR6133531.sra Written 197444 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra Rejected 197427 READS because READLEN < 1 Read 197427 spots for ERR6133531.sra Written 197427 spots for ERR6133531.sra SRR ids: ['ERR6133531.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_27ik1dys ERR6133531.sra spots: 3948557 blocks: [[1, 197427], [197428, 394854], [394855, 592281], [592282, 789708], [789709, 987135], [987136, 1184562], [1184563, 1381989], [1381990, 1579416], [1579417, 1776843], [1776844, 1974270], [1974271, 2171697], [2171698, 2369124], [2369125, 2566551], [2566552, 2763978], [2763979, 2961405], [2961406, 3158832], [3158833, 3356259], [3356260, 3553686], [3553687, 3751113], [3751114, 3948557]] ERR6133531 file size 873964 ERR6133531 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR6133531 ERR6133531_1.fastq Input file: ERR6133531_1.fastq trimmed: ERR6133531-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 08:03:21 2024 >> started Sat Dec 7 08:03:23 2024 >> done (1.995s) 3948557 reads processed; of these: 39 ( 0.00%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 3948507 (100.00%) reads available; of these: 75137 ( 1.90%) trimmed reads available after processing 3873370 (98.10%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 17 0.00% 20 1 0.00% 21 2 0.00% 22 5 0.00% 23 2 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 5 0.00% 28 1 0.00% 29 32 0.00% 30 5 0.00% 31 2 0.00% 32 7 0.00% 33 5 0.00% 34 12 0.00% 35 19 0.00% 36 446 0.01% 37 6 0.00% 38 16 0.00% 39 12 0.00% 40 28 0.00% 41 14 0.00% 42 6 0.00% 43 9 0.00% 44 5 0.00% 45 3 0.00% 46 4 0.00% 47 9 0.00% 48 5 0.00% 49 1 0.00% 50 3 0.00% 51 15 0.00% 52 2 0.00% 53 3 0.00% 54 3 0.00% 55 4 0.00% 56 6 0.00% 57 9 0.00% 58 4 0.00% 59 4 0.00% 60 7 0.00% 61 8 0.00% 62 1 0.00% 63 4 0.00% 64 2 0.00% 65 8 0.00% 66 4 0.00% 67 10 0.00% 68 35 0.00% 69 100 0.00% 70 6722 0.17% 71 6081 0.15% 72 6257 0.16% 73 5856 0.15% 74 6074 0.15% 75 6002 0.15% 76 5304 0.13% 77 5737 0.15% 78 6389 0.16% 79 7271 0.18% 80 6712 0.17% 81 7715 0.20% 82 8272 0.21% 83 8208 0.21% 84 7132 0.18% 85 181 0.00% 86 340 0.01% 87 526 0.01% 88 961 0.02% 89 1878 0.05% 90 4278 0.11% 91 12745 0.32% 92 51834 1.31% 93 3775113 95.61% 3948507 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=36 prefix-density=0.31 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=67.97 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=6.3 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGT Started job on | Dec 07 08:03:34 Started mapping on | Dec 07 08:03:34 Finished on | Dec 07 08:03:40 Mapping speed, Million of reads per hour | 2369.10 Number of input reads | 3948507 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2811729 Uniquely mapped reads % | 71.21% Average mapped length | 92.23 Number of splices: Total | 139304 Number of splices: Annotated (sjdb) | 114687 Number of splices: GT/AG | 134070 Number of splices: GC/AG | 3464 Number of splices: AT/AC | 79 Number of splices: Non-canonical | 1691 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.84 Insertion rate per base | 0.02% Insertion average length | 2.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1050267 % of reads mapped to multiple loci | 26.60% Number of reads mapped to too many loci | 26008 % of reads mapped to too many loci | 0.66% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.49% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 86511 86511 86511 N_multimapping 1050267 1050267 1050267 N_noFeature 202843 231580 2688621 N_ambiguous 107761 13386 342 UnstrandedReadsAssigned:2501125 PositiveStrandReadsAssigned:2566763 NegativeStrandReadsAssigned:122766 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133531 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133531-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,948,507 reads, 3,314,658 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,107 rounds 52973 ERR6133531.ke.tsv 35125 ERR6133531.se.tsv 88098 total ==> ERR6133531.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 148 42.9752 PNS24243 293 194 0 0 KQK14069 1603 1504 140 37.0844 KQK14071 474 375 0 0 ==> ERR6133531.se.tsv <== BRADI_1g14170v3 141 BRADI_1g53295v3 15 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 110 BRADI_1g48960v3 0 ERR6133531 completed mapping pipeline successfully